HEADER DNA 02-NOV-18 6IP7 TITLE STRUCTURE OF HUMAN TELOMERIC DNA WITH 5-SELENOPHENE-MODIFIED TITLE 2 DEOXYURIDINE AT RESIDUE 11 COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (22-MER); COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 4 ORGANISM_TAXID: 9606 KEYWDS HUMAN TELOMERE, PARALLEL G-QUADRUPLEX, DNA EXPDTA X-RAY DIFFRACTION AUTHOR K.SAIKRISHNAN,A.NUTHANAKANTI,S.G.SRIVATSAN,I.AHMAD REVDAT 4 22-NOV-23 6IP7 1 LINK REVDAT 3 24-JUL-19 6IP7 1 JRNL REVDAT 2 05-JUN-19 6IP7 1 JRNL REVDAT 1 15-MAY-19 6IP7 0 JRNL AUTH A.NUTHANAKANTI,I.AHMED,S.Y.KHATIK,K.SAIKRISHNAN, JRNL AUTH 2 S.G.SRIVATSAN JRNL TITL PROBING G-QUADRUPLEX TOPOLOGIES AND RECOGNITION CONCURRENTLY JRNL TITL 2 IN REAL TIME AND 3D USING A DUAL-APP NUCLEOSIDE PROBE. JRNL REF NUCLEIC ACIDS RES. V. 47 6059 2019 JRNL REFN ESSN 1362-4962 JRNL PMID 31106340 JRNL DOI 10.1093/NAR/GKZ419 REMARK 2 REMARK 2 RESOLUTION. 1.55 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.10.1_2155: ???) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.55 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 48.92 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.960 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 3 NUMBER OF REFLECTIONS : 21923 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.191 REMARK 3 R VALUE (WORKING SET) : 0.189 REMARK 3 FREE R VALUE : 0.213 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.090 REMARK 3 FREE R VALUE TEST SET COUNT : 1115 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 48.9401 - 3.0999 0.99 2567 179 0.1559 0.1946 REMARK 3 2 3.0999 - 2.4605 1.00 2589 156 0.2093 0.2211 REMARK 3 3 2.4605 - 2.1494 1.00 2620 136 0.2043 0.1827 REMARK 3 4 2.1494 - 1.9529 1.00 2602 134 0.2313 0.2605 REMARK 3 5 1.9529 - 1.8129 1.00 2597 150 0.2344 0.2710 REMARK 3 6 1.8129 - 1.7060 1.00 2632 98 0.1967 0.3095 REMARK 3 7 1.7060 - 1.6206 0.99 2579 120 0.2007 0.2076 REMARK 3 8 1.6206 - 1.5500 0.99 2622 142 0.2607 0.2684 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.160 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 25.000 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.012 529 REMARK 3 ANGLE : 1.424 819 REMARK 3 CHIRALITY : 0.073 86 REMARK 3 PLANARITY : 0.012 23 REMARK 3 DIHEDRAL : 29.814 212 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: SF FILE CONTAINS FRIEDEL PAIRS UNDER REMARK 3 F_MINUS AND F_PLUS COLUMNS. REMARK 4 REMARK 4 6IP7 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 14-NOV-18. REMARK 100 THE DEPOSITION ID IS D_1300009668. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 18-FEB-16 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I02 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9795 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M-F REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 22608 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.550 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 12.50 REMARK 200 R MERGE (I) : 0.05800 REMARK 200 R SYM (I) : 0.05800 REMARK 200 FOR THE DATA SET : 23.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.55 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.58 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.89800 REMARK 200 R SYM FOR SHELL (I) : 0.89800 REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: 1KF1 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 55.54 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.77 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.05M POTASSIUM CACODYLATE (PH7.2), REMARK 280 0.625M AMMONIUM ACETATE, 0.2M KCL, 15% PEG400, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 6 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z REMARK 290 3555 -X+Y,-X,Z REMARK 290 4555 -X,-Y,Z REMARK 290 5555 Y,-X+Y,Z REMARK 290 6555 X-Y,X,Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 50 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 4530 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 0.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 K K A 103 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 221 LIES ON A SPECIAL POSITION. REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 DG A 2 O3' DG A 2 C3' -0.041 REMARK 500 DG A 3 O3' DG A 3 C3' -0.041 REMARK 500 AWC A 11 O3' DT A 12 P -0.103 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 K A 102 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DG A 2 O6 REMARK 620 2 DG A 3 O6 73.9 REMARK 620 3 DG A 8 O6 69.2 90.3 REMARK 620 4 DG A 9 O6 130.6 70.1 78.1 REMARK 620 5 DG A 14 O6 108.0 156.0 69.2 92.9 REMARK 620 6 DG A 15 O6 156.9 112.5 130.9 70.7 75.5 REMARK 620 7 DG A 20 O6 69.9 130.4 106.8 157.8 69.7 90.9 REMARK 620 8 DG A 21 O6 90.3 71.4 155.9 108.7 131.7 72.1 75.9 REMARK 620 N 1 2 3 4 5 6 7 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 K A 103 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DG A 2 O6 REMARK 620 2 DG A 2 O6 0.0 REMARK 620 3 DG A 8 O6 68.8 68.8 REMARK 620 4 DG A 8 O6 68.8 68.8 0.0 REMARK 620 5 DG A 14 O6 108.3 108.3 68.9 68.9 REMARK 620 6 DG A 14 O6 108.3 108.3 68.9 68.9 0.0 REMARK 620 7 DG A 20 O6 70.4 70.4 107.0 107.0 70.3 70.3 REMARK 620 8 DG A 20 O6 70.4 70.4 107.0 107.0 70.3 70.3 0.0 REMARK 620 N 1 2 3 4 5 6 7 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 K A 101 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DG A 3 O6 REMARK 620 2 DG A 4 O6 70.9 REMARK 620 3 DG A 9 O6 66.0 89.2 REMARK 620 4 DG A 10 O6 125.9 78.7 70.1 REMARK 620 5 DG A 15 O6 98.9 154.8 65.7 90.1 REMARK 620 6 DG A 16 O6 155.8 126.6 124.6 77.1 71.2 REMARK 620 7 DG A 21 O6 66.7 125.1 103.3 155.8 66.5 89.1 REMARK 620 8 DG A 22 O6 90.2 75.9 155.2 124.5 128.2 79.9 71.1 REMARK 620 N 1 2 3 4 5 6 7 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue K A 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue K A 102 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue K A 103 DBREF 6IP7 A 1 22 PDB 6IP7 6IP7 1 22 SEQRES 1 A 22 DA DG DG DG DT DT DA DG DG DG AWC DT DA SEQRES 2 A 22 DG DG DG DT DT DA DG DG DG HET AWC A 11 36 HET K A 101 1 HET K A 102 1 HET K A 103 1 HETNAM AWC 2'-DEOXY-5'-O-[(R)-HYDROXY(OXO)-LAMBDA~5~-PHOSPHANYL]- HETNAM 2 AWC 5-SELENOPHEN-2-YLURIDINE HETNAM K POTASSIUM ION FORMUL 1 AWC C13 H15 N2 O7 P SE FORMUL 2 K 3(K 1+) FORMUL 5 HOH *50(H2 O) LINK O3' DG A 10 P DAWC A 11 1555 1555 1.59 LINK O3'DAWC A 11 P DT A 12 1555 1555 1.50 LINK O6 DG A 2 K K A 102 1555 1555 2.85 LINK O6 DG A 2 K K A 103 1555 1555 2.85 LINK O6 DG A 2 K K A 103 1555 4665 2.85 LINK O6 DG A 3 K K A 101 1555 1555 2.94 LINK O6 DG A 3 K K A 102 1555 1555 2.72 LINK O6 DG A 4 K K A 101 1555 1555 2.68 LINK O6 DG A 8 K K A 102 1555 1555 2.80 LINK O6 DG A 8 K K A 103 1555 1555 2.82 LINK O6 DG A 8 K K A 103 1555 4665 2.82 LINK O6 DG A 9 K K A 101 1555 1555 2.90 LINK O6 DG A 9 K K A 102 1555 1555 2.81 LINK O6 DG A 10 K K A 101 1555 1555 2.75 LINK O6 DG A 14 K K A 102 1555 1555 2.83 LINK O6 DG A 14 K K A 103 1555 1555 2.82 LINK O6 DG A 14 K K A 103 1555 4665 2.82 LINK O6 DG A 15 K K A 101 1555 1555 2.97 LINK O6 DG A 15 K K A 102 1555 1555 2.68 LINK O6 DG A 16 K K A 101 1555 1555 2.70 LINK O6 DG A 20 K K A 102 1555 1555 2.80 LINK O6 DG A 20 K K A 103 1555 1555 2.77 LINK O6 DG A 20 K K A 103 1555 4665 2.77 LINK O6 DG A 21 K K A 101 1555 1555 2.89 LINK O6 DG A 21 K K A 102 1555 1555 2.77 LINK O6 DG A 22 K K A 101 1555 1555 2.71 SITE 1 AC1 9 DG A 3 DG A 4 DG A 9 DG A 10 SITE 2 AC1 9 DG A 15 DG A 16 DG A 21 DG A 22 SITE 3 AC1 9 K A 102 SITE 1 AC2 10 DG A 2 DG A 3 DG A 8 DG A 9 SITE 2 AC2 10 DG A 14 DG A 15 DG A 20 DG A 21 SITE 3 AC2 10 K A 101 K A 103 SITE 1 AC3 5 DG A 2 DG A 8 DG A 14 DG A 20 SITE 2 AC3 5 K A 102 CRYST1 56.483 56.483 42.415 90.00 90.00 120.00 P 6 6 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.017704 0.010222 0.000000 0.00000 SCALE2 0.000000 0.020443 0.000000 0.00000 SCALE3 0.000000 0.000000 0.023577 0.00000